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DECEMBER 2017

RESEARCH Evaluating the Aquatic Habitat Potential of Flooded Polders in The Sacramento–San Joaquin Delta John R. Durand *, 1

NSBI predictions. Because flood probabilities and Volume 15, Issue 4 | Article 4 https://doi.org/10.15447/sfews.2017v15iss4art4 repair prioritization analyses suggest that polders in the south Delta are most likely to flood and be * Corresponding author: [email protected] abandoned, without extensive intervention, much of 1 Center for Watershed Sciences, University of –Davis, the Delta will become a freshwater lake ecosystem, Davis, CA 95616 dominated by alien . Proactive management of flooded tracts will nearly always hedge risks, save money, and offer more functional habitats ABSTRACT in the future; however, without proper immediate incentives, it will be difficult to encourage strong Large tracts of land in the Sacramento–San Joaquin management practices. Delta are subsided because of agricultural practices, creating polders up to 10 m below sea level that are vulnerable to flooding. As protective dikes breach, KEY WORDS these become shallow, open-water habitats that Polder, flooded island, restoration, reconciliation will not resemble any historical state. I investigated ecology, novel ecosystems, Sacramento–San Joaquin physical and biotic drivers of novel flooded polder Delta habitat, using a Native Species Benefit Index (NSBI) to predict the nature of future Delta ecosystems. Results suggest that flooded polders in the north INTRODUCTION Delta will have the ecology and fish community Twentieth-century land-use practices have accelerated composition of a tidal river plain, those in the Cache– land subsidence and polder formation around the Lindsey Complex (CLC) will have that of a tidal globe, especially where is combined backwater, those in the confluence of the Sacramento with intensive near rivers and and San Joaquin rivers a brackish , and (McCreary et al. 1992; Lindenschmidt et al. 2009). those in the south Delta a freshwater lake. Flooded Amid rising sea levels, there is growing concern east-side Delta polders will likely be a transitional about how or whether to manage these lands against zone between south Delta lake-like ecosystems flooding. Increasing pressure on will result in and north Delta tidal river plains. I compared each flooding and permanent land loss, but little is known regional zone with the limited available literature about what will become of these flooded polders once and data on local fish assemblies to find support for ESTUARY & WATERSHED SCIENCE VOLUME 15, ISSUE 4, ARTICLE 4 they are inundated. These lands are highly altered METHODS from their original form, and will form novel aquatic habitats with largely unknown consequences for Site Description resident species. The convergence of the Sacramento and San In the Sacramento–San Joaquin Delta (Delta), islands Joaquin rivers forms the tidal freshwater Delta, a were historically reclaimed from or network of braided channels separated from the emergent marsh habitat by building levees, sea by the brackish and salt water embayments of channels, and draining the land. Subsidence was the San Francisco Estuary (estuary) (Conomos et al. accelerated by soil oxidation and compaction from 1985). The Delta consists of at least four distinct agriculture, reducing elevation as much as eight m hydrodynamic provinces (Whipple et al. 2012): the below sea level in some cases (Weir 1950; Mount south, north, and eastern Delta each have different and Twiss 2005). These polders are vulnerable freshwater sources, while the western Delta is to flooding when levees collapse because o poor influenced by brackish water from . Flow building materials, age, floods, earthquakes, and patterns and timing, soil types, geomorphology, and sea level rise (Thompson 1957, p. 19; Suddeth et al. riparian vegetation differ among the regions. 2010; Suddeth 2011). The area potentially affected The Delta has been developed into a hub of by flooding in the Delta is substantial: approximately agriculture and water transport since the 1850s. 140,000 hectares of land are at or above sea level, Intense usage caused Delta islands to be transformed and the area of vulnerability will increase over the into polders, which are protected from flooding next several decades with sea level rise. Many polders by a network of peat and riprapped levees. The have already flooded and been reclaimed over the resulting inverted landscape is shown in Figure 1, past century. Several have been abandoned because it where waterways are elevated at or above sea level, proved uneconomical to resuscitate them, or because and adjacent farmed polders are well below; in this they were targeted as environmental restoration landscape, boaters look over the and downhill projects. The largest of these include Franks Tract, to see farmhouses and fields. , and Liberty Island (Logan 1990; Suddeth et al. 2010). The physical habitat conditions Subsidence has led to increasing pressure on and biota of currently abandoned flooded polders dikes, which vary in construction and reliability in the Delta are varied, but the evolution from (Thompson 1957), leading to regular dike failure and polder to flooded habitat is poorly understood, and flooding (URS/JBA 2008; Suddeth et al. 2010). A has not been methodically studied. While there is number of tracts have been permanently abandoned considerable political will to restore parts of the in this way, including Sherman Lake, Big Break, Little Delta to support native fishes that are threatened or , Franks Tract, Mildred Island, and endangered (ICF International 2013), how flooded Liberty Island. Other polders, such as Prospect Island polders will support or work against these goals is and McCormick–Williamson Tract (which failed and poorly understood. was reclaimed in 2017), have been acquired with the intent to flood as mitigation for Delta water export To address this gap in understanding, I developed and associated entrainment and mortality of Delta a Native Species Benefit Index (NSBI) to evaluate and . Decisions to repair are based upon flooded polder ecosystems using just elevation, land value, infrastructure, population density, and hydrodynamic flow, and turbidity. I wanted to importance to water management (Suddeth et al. address the questions: 2010; Suddeth 2011). 1. How will these factors determine the development of novel aquatic habitat after polder flooding? Ecological Characterization 2. What regional differences can be expected from Historically, the Delta was characterized by intertidal flooded polder habitat? and emergent marsh habitat, connected by an extensive channel network (Whipple et al. 2012). Anthropogenic alteration, drought, and species

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Figure 1 Poldered islands in the Sacramento-San Joaquin Delta, viewed as a digital elevation model overlain with satellite imagery and with vertical relief exaggerated 10x. Two large permanently flooded polders are shown on the left half of the image. The other tracts range from 3-8 meters below sea level. Irregularities in polder surfaces are due to orchard crops, dikes, and buildings (Image credit: Burak Yikilmaz). invasions have created a novel ecosystem without decline (O’Rear and Moyle 2010; personal data historical precedent, dominated by open-water 2007–2016). In addition, , the CLC, and habitat, few , and a mix of native and Liberty Island have had much more limited invasions invasive alien species (Moyle et al. 1986; Nichols et of submersed aquatic vegetation (SAV) and clams al. 1986). During the drought of 1987–94, a number (personal observations 2007–2016; Baumsteiger et al. of alien species were introduced to the Delta, and 2017). previously expanded their range. Regional and local differences are likely to influence The alien clams Potamocorbula amurensis (Nichols how polders develop into aquatic habitat. For et al. 1990; Kimmerer 2004; Winder and Jassby example, when deeply subsided polders flood, tidally 2010; Winder et al. 2011) and Corbicula fluminea influenced lake-like environments are created. These (Hymanson et al. 1994) spread throughout the Delta are characterized by low-energy flood-dominated and Suisun Bay, causing chronic phytoplankton flows, high residence times, warm water, limited depletion. The submersed aquatic weed Egeria densa physical structure or structure provided by SAV, expanded its range, altering the structure and and mostly alien fishes dominated by the family function of open-water tracts and slow-moving Centrarchidae (Lucas et al. 2002; Nobriga et al. 2005; sloughs (Grimaldo and Hymanson 1999; Toft 2000; Young et al. 2011). When shallow polders flood, Brown 2003; Durand et al. 2016). By 2000, pelagic dynamic ebb-dominated flow patterns may create organisms had greatly declined in the upper estuary habitats with higher pelagic productivity, emergent (Sommer et al. 2007). However, not all regions of the intertidal or seasonal marsh, stands of SAV, and a Delta have responded in the same way. Suisun Marsh diverse fish assembly that includes a mix of natives has been largely unaffected by the pelagic organism and aliens (Simenstad et al. 2000; Nobriga et al.

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2005; Nobriga and Feyrer 2007; McLain and Castillo anadromous fishes on spawning migrations. 2010; Young et al. 2011), providing a more desirable Tidal energy creates mixed residence times along outcome. longitudinal gradients, which promote diversity and exchange of pelagic food web constituents and Given the extent of subsided lands, it is important fish. In contrast, regions with low hydrodynamic to understand the physical differences among energy create lake-like environments that tend to be potentially flooded habitats to predict future dominated by alien fishes and aquatic plants, lack environmental outcomes in the Delta. These are directional flows to support anadromous fishes, and linked to a number of biological outcomes, including have limited capacity to support and export pelagic phytoplankton production, emergent vegetation food resources (Lucas et al. 1999a, 2002; Jones et al. growth, harmful formation, alien 2008; Lehman et al. 2008, 2009; Fleenor et al. 2010; aquatic vegetation growth, zooplankton production, Durand 2015). and dispersal and pelagic fish suitability. The key physical drivers of elevation, hydrodynamic flow, Turbidity provides cover for larval and juvenile and turbidity are likely to have outsized effect on native fishes, and adult . Clear water the biological outcome of flooding polders and are makes fish more vulnerable to predation by visual discussed below. predators. Smelt, larval, and juvenile fishes follow high-turbidity zones behaviorally, seeking refuge. Gradients of elevation can create habitat complexity Many native fishes are adapted to live under high- that may accommodate a variety of aquatic species. turbidity conditions by foraging on benthos. Invasive At intertidal or shallow water elevations, tidal centrarchids, in contrast, are adapted to foraging in energy can interact with physical features to create clear water on structural elements, such as wood or a dynamic environment. Complex hypsometry can SAV (Grimaldo and Hymanson 1999; Toft et al. 2003; create refuges for fish and mixed residence times Feyrer and Healey 2003; Nobriga and Feyrer 2007; that promote pelagic food production. Shallow water Ferrari et al. 2014). can produce high concentrations of phytoplankton under certain conditions, supporting the pelagic food web. Shallow and intertidal elevations with emergent Native Species Benefit Index marsh vegetation may also support both pelagic I used available data for depth, hydrodynamic flows, and demersal food webs. In contrast, polders with and turbidity to create a simple metric for polder elevations much below sea level may create open- evaluation. These factors allowed comparison of water habitat that dissipates tidal energy and leaves individual and regional differences among polders. little physical surface for tides to work against. Such Because most of the polders being evaluated are not habitat becomes more vulnerable to invasion by SAV flooded, elevation was the easiest metric to evaluate like E. densa, which can change habitat dynamics. on an individual basis. Using a hydrodynamic Unless deep open-water habitat stratifies, it is model, I estimated potential hydrodynamic energy unlikely to promote phytoplankton blooms, in part as flow from adjacent point locations in channels. I because water circulates below the depth critical for estimated turbidity using continuous monitoring data photosynthesis (Simenstad et al. 1999, 2000; Lucas from multiple stations in adjacent to create regional et al. 2002; Lopez et al. 2006; Ahearn et al. 2006; estimates. Of course, each potentially flooded polder Thompson et al. 2008; Moyle et al. 2010; Whipple et will have a unique geographic relationship to Delta al. 2012; Enright et al. 2013). hydrodynamics and climate, based upon location, The timing and magnitude of hydrodynamic structural morphology, number of breaches, and energy from tidal and riverine flows affect pelagic hydrodynamics. More explicit evaluation will require productivity, exchange of nutrients, and transport collection of data and modeling specific to each of food resources and pelagic organisms. Flow polder. The NSBI is a simple way to easily assess energy can discourage alien species that can alter differences among 78 different Delta polders, all of the ecosystem, such as aquatic plants and sunfishes. which have some potential to breach and flood. Ebb-dominated flows help direct migratory and

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I evaluated diked reclamation districts in the Delta Table 1 Elevation scores region that had areas within or below the intertidal zone (0–1.5 m above mean lower low water [MLLW]). Depth Primary I considered reclamation districts that had elevations (m above MLLW) Category points greater than 1.5 m above MLLW to be above the < -1.5 Subtidal Deep 0 intertidal range, and removed them from the analysis. -1.5 — -0.1 Subtidal Shallow 1 Some of these, like Yolano and Peters Pocket, may 0 — 1.5 Intertidal 3 provide amenable floodplain habitat if levees were Depth range Secondary removed. Peters Pocket, along with some other tracts, (m above MLLW) points has a high probability of becoming intertidal with Range crosses < -1.5 Subtidal Deep 0 sea level rise. However, these “high-elevation” tracts Range crosses -1.5 — -0.1 Subtidal Shallow 0.5 were outside the scope of this study. I also removed Range crosses 0 — 1.5 Intertidal 1.5 reclamation districts west of the confluence of the Range crosses >1.5 Emergent 1 San Joaquin and Sacramento rivers (the Confluence), and urbanized reclamation districts from the analysis. I used the following approaches to create metrics of depth, flow energy, and turbidity. Hydrodynamic Energy Depth I used estimated flow data from an RMA2 model (King 1988) for water years 1998, 2003, 2006, 2007, I used U.S. Geological Survey (USGS) topographic and 2008 at 20 different locations across the Delta maps (USGS 2000), a digital elevation map from (W. Fleenor, 2012 unpublished data, see "Notes"). 2007–08 Light Detection and Ranging (LiDAR) data Average daily flows (cfs) varied considerably (Dudas 2010), and a continuous surface elevation among years with different hydrologic regimes map of the Delta (Wang and Ateljevich 2012) to (e.g., wet winters with high directional flows tend determine elevation relative to MLLW (NAVD 88). to create differences in riverine flow-dominated Elevation and reclamation districts are shown in channels, while tidally-dominated channels remained Figure 2. I used these data to assess the commonest relatively unaffected). I used Ward’s Method to elevations on each tract, and the upper and lower create correlations among sites that I plotted as a limits. I classified depths as follows: elevations more cluster dendogram (Figure 3). I then used clusters than 1.5 m below MLLW were subtidal deep water; to plot daily flows as yearly time–series to confirm elevations more than zero and less than 1.5 m below distinct patterns for geographic flow regions (e.g., MLLW were subtidal shallow water; elevations greater Figure 4). Using amplitude of the plots, I assigned than zero and less than 1.5 meters above MLLW points to the resulting eight flow regions on a scale were intertidal. I assigned each category points in of 1 through 8, where 1 was for the lowest flow proportion to the presumed benefits provided to energy and 8 for the highest flow. I assigned polders desirable ecosystem processes. Polders received both to a flow region to receive a score, which was primary and secondary points to represent the varied standardized to one (Table 2). Regions and scores are topography of each polder (Table 1). I gave primary shown in Figure 5. depth points for the commonest elevation category. I gave secondary depth points for the categories crossed by the maximum and minimum elevations Turbidity for each polder. I tallied points tallied for each tract To evaluate turbidity, I extracted averaged daily and divided by six, the maximum points possible, turbidity estimates from 51 water quality stations which normalized scores to one. deployed throughout the Delta for the time–period from 2006 through 2012. I downloaded data from the California Data Exchange Center (CDEC) website (http://cdec.water.ca.gov/cgi-progs/queryCSV, CDWR 2013). I plotted the time–series and found a high

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Figure 2 Delta polders and hypsometry (elevation in m above MLLW). White areas are artifacts of LIDAR survey data and post-processing, or elevations above 6 m. degree of consistency in stations within regions turbidity region and 5 being the highest. I then (Figure 6). To create a regional index of relative divided scores by five to standardize to one. turbidity, I took simple means of the daily average To calculate the NSBI score, I scored each polder for each station from 2009 through 2012 (which from 0 to 3 by adding the three metrics (Table 4). included the most complete records) and mapped The NSBI assumes no difference in relative benefits each station with its representative mean turbidity among the three factors. By weighting potential value (Figure 7). Using these stations as guides, I benefits equally, I provide a simple way to evaluate designated ten different geographic regions as having key conditions that drive different ecological distinct patterns of turbidity. I scaled these regions outcomes, and ranked them as percentiles. I mapped according to Table 3, with 1 being the lowest- the top and bottom 25% scores for the three

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Figure 3 Cluster dendogram showing flow relationships among sloughs

Table 2 Flow regions, flow query sites, and scores combined metrics to understand regional trends (Figures 8 and 9). Region Sites Abbreviation Points In addition to NSBI Score and Percent Rank for each at Bacon polder, I tabulated Current Status, recommended Lower Old River at Victoria OldatVic South Delta 0 Flood Response, Probability of Failure, and Middle River Middle Victoria Vic Reclamation District number (Table 4). Current Status indicated whether a polder is flooded, managed as a Disappointment Disappointment Slough Disappt 1 , or non-flooded as of 2017. Flood Response Cache Slough gives the recommended action to be taken if levees Cache Lindsey Slough Cache Complex Lindsey 2 fail and polders flood from Suddeth et al. (2010), Sacramento Deep Water SCWC and repair prioritization rankings from the Delta Ship Channel Risk Management Strategy (URS/JBA 2008) based Suisun Not included 3 upon the value of each polder to Delta operations and salinity control. Probability of Failure was North Fork Mokelumne NFMok East Side North 4 South Fork Mokelumne SFMok also taken from Suddeth et al. (2010) and the Spud Delta Risk Management Strategy (URS/JBA 2008). East Side South RandR 5 Colored highlights indicate geographic regions: Middle River at Old River MRatOR red = Confluence, orange = north Delta, yellow = CLL Sacramento– Steam 6 Complex, green = east Delta, blue = south Delta, which Steamboat above Sac were assigned to polders only in the top and bottom Rio Vista 25% ranks. SJR Central Jersey Point Jersey 7 Delta at Twitch Prisoner RESULTS Prisoners Point Confluence Chipps 8 The highest-scoring polders came largely from the Emmaton Emma region of the Confluence, followed by polders from Rio Vista RV CLC and the north Delta (Figure 8). Polders in the

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Figure 4 Modeled flows (cfs) at selected locations (shown in legend boxes) from a representative water year (October 1, 2002–September 30, 2003), clustered together by the following regions: (A) Confluence, (B) SJR Central Delta, (C) Sacramento/Steamboat, (D) East Side South, (E) East Side North, (F) Cache–Lindsey Complex, (G) Disappointment Slough, and (H) South Delta. Additional years were plotted separately with similar results.

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Figure 5 Flow regions by color. Corresponding points and names are in the legend. Sites where flows were modeled are indicated by black hexagons and named on the map. Note that tidal wetlands in Suisun Marsh were not evaluated in this study.

9 https://doi.org/10.15447/sfews.2017v15iss4art4 SAN FRANCISCO ESTUARY & WATERSHED SCIENCE VOLUME 15, ISSUE 4, ARTICLE 4 log (Turbidity) (ntu) log (Turbidity)

Figure 6 Turbidity (ntu) for 51 stations throughout the Delta from 2006-2012. Colors represent blocks of CDEC stations from similar geographic locations.

Table 3 Regional turbidity means and scores region as Tidal Backwater, and in the north Delta as Tidal River Plain. Turbidity (ntu) Points The lowest-scoring tracts came primarily from the 5—9 1 east and south Delta (Figure 9). Nearly all of these tracts occur in the clearest water in the Delta. 10—14 2 Most are subsided below sea level, deepening with 15—19 3 proximity to the San Joaquin River corridor. The east-side polders have elevation gradients that are 20—29 4 probably desirable for some wetland and subtidal 30+ 5 restoration purposes, but they are limited by low flows and clear water. The south Delta polders have clear water, deep subsidence, and flows strongly north Delta and the Confluence scored high because affected by large south Delta water export pumping of their proximity to flows from the Sacramento plants, giving these the lowest scores. I classified River. The CLC has lower flow energy because it is habitats in the east Delta region as a Transition Zone, mostly tidal, but received high scores for turbidity and in the south Delta region as Freshwater Lake. and shallow depth. Differences among these three regions can be summarized as a series of trade- The tracts not in the top or bottom 25% of scores offs among the three criteria that lead to differing represent a range of conditions that overlap among ecological outcomes (Table 5). I classified habitat in regions. For example, although the polders adjacent the Confluence as Low Salinity Estuary, in the CLC to the San Joaquin River are generally the most subsided, many of these tracts did not score in

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Figure 7 Turbidity regions in the Delta, averaged from CDEC values from 2009 through 2012

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Table 4 Polders with NSBI score and percent rank. Current status is indicated by F = Flooded, F* = Intentional flooding planned; MW = Managed wetland; and intact if blank. Flood response gives the recommended response and priority of a number of polders: R = High value, repair if flooded; NR = Do not repair if flooded (Suddeth et al. 2010); U = Unsure. Numbers show repair priority where 1 = highest priority, and 69 is lowest (URS/JBA 2008). RD is reclamation district.

Percent Probability of Polder Score rank Current status Flood response failure RD Sherman Lake 2.52 0.99 F — — 2.30 0.96 MW ? 0.07 RD 1607 Winter Island 2.30 0.96 MW ? RD 2122 Netherlands 2.27 0.95 ? 0.03 RD 999 Little 2.17 0.94 F — — Donlon Island 2.10 0.92 F — — Liberty Island 2.08 0.91 F — — RD 2093 Libby McNeil District 2.07 0.89 ? 0.01 RD 369 Merrit Island 2.07 0.89 ? 0.01 RD 150 2.00 0.86 64 0.01 RD 2060 2.00 0.86 ? 0.03 RD 2098 Egbert Tract 1.97 0.85 63 0.01 RD 536 Rough and Ready Island 1.94 0.84 45 0.03 Stockton Ehrheardt Club 1.90 0.82 — 0.01 RD 813 Lisbon District 1.89 0.81 — 0.03 RD 307 Little Egbert Tract 1.88 0.80 62 0.03 RD 2084 Prospect Island 1.85 0.78 F* — — RD 1667 Grand Island 1.82 0.75 R / 40 0.03 RD 3 Pierson District 1.82 0.75 42 0.01 RD 551 Sutter Island 1.82 0.75 41 0.01 RD 349 Cache Pocket 1.75 0.72 MW ? French Island 1.75 0.72 ? Fern / Headreach / Tule islands 1.74 0.71 F — — New Hope Tract 1.70 0.70 54 0.07 RD 348 1.69 0.68 R / 23 0.05 RD 684 / 524 / 544 Sherman Island 1.68 0.67 R / 38 0.07 RD 341 Little Venice 1.58 0.66 F — — Little Franks Tract 1.53 0.65 F — — McCormack–Williamson Tract 1.45 0.63 F* — 0.03 RD 2110 Little Hastings Tract 1.42 0.62 F — — Big Break 1.40 0.59 F — — Veale Tract 1.40 0.59 18 0.01 RD 2065 Franks Tract 1.36 0.54 F — — 1.36 0.54 NR / 36 / 36 0.09 RD 2059 1.36 0.54 NR / 37 / 37 0.01 RD 830 1.36 0.54 NR / 34 / 34 0.1 RD 2026 Twitchell Island 1.28 0.53 NR / 35 / 35 0.05 RD 1601

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Table 4 Polders with NSBI score and percent rank (Continued)

Percent Probability of Polder Score rank Current status Flood response failure RD 1.23 0.52 R / 61 0.03 RD 501 Brack Tract 1.20 0.51 R / 65 0.05 RD 2033 Bishop Tract 1.16 0.49 67 0.01 RD 2042 Brannan- 1.15 0.47 R / 33 0.05 RD 2067 / 317 / 407 / 556 Fabian Tract 1.15 0.47 10 0.01 RD 773 Mandeville Island 1.08 0.44 NR / 26 / 26 0.05 RD 2027 Venice Island 1.08 0.44 NR / 31 / 31 0.07 RD 2023 Hotchkiss Tract 1.07 0.42 20 0.03 RD 799 Union Island 1.07 0.42 U / 8 0.01 RD 1/2 Tyler Island 0.98 0.41 NR / 60 / 60 0.07 RD 563 0.95 0.38 R / 66 0.03 RD 2086 0.95 0.38 U / 39 0.03 RD 548 Wright–Elmwood 0.91 0.37 U / 4 0.01 RD 2119 McDonald Island 0.83 0.32 NR / 25 / 25 / 30 0.05 RD 2030 0.83 0.32 NR / 30 / 30 0.05 RD 2041 0.83 0.32 NR / 27 / 27 / 27 0.03 RD 2037 Rio Blanco Tract 0.83 0.32 68 0.01 RD 2114 0.78 0.30 NR 0.01 RD 2111 Holland Tract 0.73 0.29 NR / 19 0.03 RD 2025 Eucalyptus Island 0.70 0.22 F — — Rhode Island 0.70 0.22 F — — 0.70 0.22 R / 32 0.03 RD 756 Byron Tract 0.70 0.22 12 0.03 RD 800 0.70 0.22 NR / 29 0.05 RD 2029 Staten Island 0.70 0.22 NR 0.05 RD 38 Coney Island 0.65 0.20 NR / 11 0.01 RD 2117 0.58 0.18 48 0.01 RD 2115 Shin Kee Tract 0.58 0.18 69 0.03 0.48 0.16 21 0.05 Drexler Tract 0.45 0.15 ? 0.05 RD 2039 0.37 0.14 ? RD 2113 0.33 0.13 NR / 28 0.01 RD 2044 0.28 0.11 U /15 0.03 RD 2024 0.20 0.01 F — — RD 2118 Mildred Island 0.20 0.01 F — — RD 2021 Bacon Island 0.20 0.01 NR / 17 0.05 RD 2028 0.20 0.01 R / 24 0.05 RD 2038 / 2039 0.20 0.01 R / 16 0.03 RD 2036 0.20 0.01 NR / 22 0.07 RD 2090 Victoria Island 0.20 0.01 U / 9 0.05 RD 2040 0.20 0.01 R / 14 0.03 RD 2072

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Figure 8 Regions dominated by high-scoring polders on the NSBI Figure 9 Regions dominated by low-scoring polders on the NSBI the bottom 25% because of the large amount of for native species. Taking into consideration the flow energy that is available to them, which could NSBI scores and the geomorphology of the regions, be used to engineer different habitat values post- the north Delta may be best suited to tidal river plain flooding. In contrast, polders north of the San restoration activities, the (CLC) as a tidal backwater Joaquin are adjacent to channels with relatively low system, the Confluence as a low-salinity estuary flows, especially in the easternmost tracts; they are mouth, the south Delta as a freshwater lake, and the shallower toward the east side of the region, and east Delta as a transition zone between lotic (north form an elevational gradient to above sea level (from Delta) and lentic (south Delta) environments. -5 m to 4 m from MLLW). Most of the middle-scoring Evaluating the ecological potential of currently non- tracts are located toward the central and southern flooded tracts allows the risks and consequences part of the Delta. of flooding to be better assessed. Polders that are currently flooded provide some validation for these DISCUSSION categories. The CLC contains Liberty Island, the Confluence includes Sherman Lake, and the south Evaluating Regional Differences Delta contains Franks Tract and Mildred Island. The The NSBI scores suggest Delta polders are clustered high scores of Liberty Island and Sherman Lake, in five geographic regions with distinctive ecological although driven by different factors, are supported functions. The highest scores describe polders that, if by surveys of fish community assembly on those flooded, would be more likely to support restoration tracts, which show comparatively high proportions and conservation goals for native fish. At the other of natives (M. Young and D. DeCarion, 2010–2017 extreme, the lowest-scoring polders would be unlikely unpublished data, see "Notes"). Likewise, low scores to provide many benefits in terms of restoration goals for Mildred Island and Franks Tract correspond to low proportions of native fishes found on those

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Table 5 Trade-offs in regional attributes and ecological outcomes

Region Flow Elevation Turbidity Mean score Ecological outcome

Confluence High Moderate Moderate 2.18 Low salinity estuary

CLC Low Shallow High 1.86 Tidal backwater

1.60 North Delta High Shallow Low Tidal River plain

1.02 Eastside Moderate Moderate Low Transition zone

South Delta Low Deep Low 0.78 Freshwater lake

tracts (and high proportions of aliens) (Nobriga patches of clams (personal data). Planktivorous fish et al. 2005; Nobriga and Feyrer 2007; J. Durand, are rare, but the ratio of adult native to alien fishes M. Young, and D. DeCarion, 2010–2017 unpublished is relatively high, perhaps the result of brackish water data, see "Notes"). It is reasonable to conclude that and high flows, which are likely to limit centrarchid non-flooded polders in these regions, with similar fish recruitment. scores, may produce similar outcomes when flooded. The second-highest scoring polders tended to be The highest-scoring polders were, in general, clustered in the north Delta region. High flows clustered in the region of the Confluence. The from the Sacramento River, moderate turbidity, and dynamic complexity and variability of this habitat, intermediate elevations cause this region to resemble and the influence of salinity, suggest that it will tidal river plain habitat, which can provide refuge behave more like a low-salinity estuary mouth and foraging opportunities for outmigrating salmon than any other Delta region. This area is typified juveniles and other riverine species. In the north, by moderate polder depth, suggesting high polders are generally shallow, deepening to the phytoplankton production will occur here at times. south. High flows will tend to disperse plankton, but However, high flows combined with high exchange emergent vegetation will provide organic matter and may cause plankton dispersal, suggesting that it structure for epibenthic invertebrates. is poor habitat for planktivorous fish. If flows are No tracts are currently flooded in the region, but constrained by dikes to increase or vary water Prospect Island will likely be the first, as part of residence time on polders, then phytoplankton Delta Restoration efforts (EcoRestore, http://resources. productivity may increase, but, given high clam ca.gov/ecorestore/california-ecorestore-projects/). abundance and river flows in the region, both pelagic Prospect, Lisbon, Netherlands, and Merrit polders productivity and biomass will be low. are all at intertidal elevations. Grand and Pierson Sherman Lake, situated at the Confluence, supports islands are sufficiently subsided that they offer less this prediction. It is exposed to the high flows intertidal structure and restoration opportunities; of the region, but is also somewhat constrained however, they may work effectively in conjunction by old levees, emergent wetlands, and reinforced with shallower flooded polders as open-water habitat, Sherman Island levees. As a result, Sherman Lake has complemented by intertidal and emergent marsh. extensive summertime SAV patches, punctuated by A key unknown is the response of invasive aquatic open water (personal observation). The combination plants (mainly E. densa) and clams (C. fluminea) to of structure and abundant detrital carbon results in a new aquatic habitats in this region. Nutrient inputs high abundance of epibenthic invertebrates. Plankton will be high, reflecting conditions in the Sacramento biomass is low, probably because of high dispersal River. Currently, the southern half of Prospect Island and advection, and because of nearby high-density is partially open to tidal incursion, and has a thick

15 https://doi.org/10.15447/sfews.2017v15iss4art4 SAN FRANCISCO ESTUARY & WATERSHED SCIENCE VOLUME 15, ISSUE 4, ARTICLE 4 bed of E. densa where it is flooded. This is likely to because of water export. The depth, a mixed water expand once the island it open to full tidal exchange. column, high concentrations of nutrients, high densities of clams, and extensive SAV will tend The CLC, with low-energy tidal flows, shallow depths, to inhibit phytoplankton production and bloom and high turbidity, has attributes that resemble a formation. Food webs will be driven by particulate tidal backwater slough. The dominance of tidal organic matter and microbial production, supporting energy may promote mixed residence times across adult fish. Water temperatures will tend to be warm the landscape (Durand 2015), promoting pelagic because of limited flow and exchange. These polders food webs. Low background nutrient levels may will be dominated largely by alien fish species that limit invasions of C. fluminea and E. densa to some prefer warm, clear water and vertical structure. degree; however, this is currently a key uncertainty. The elevation gradient of the region will support the Franks Tract and Mildred Island, both flooded, development of emergent marsh adjacent to open characterize this region and are consistent with NSBI shallow water in places, supplying organic carbon predictions. Franks is less deep than Mildred, and to the microbial food web. Shallow water tule and has patchy distribution of SAV. Mildred is ringed by edge structure will provide a substrate for epibenthic a band of SAV along the shallower edge. The open invertebrates. The region could provide good habitat water and adjacent sites have high densities of clams for planktivorous, benthic, and piscivorous fish. (Lucas et al. 2002). Mildred Island has been known to have occasional phytoplankton blooms, but these are Liberty Island, the major flooded polder in the CLC, consumed upon export by high densities of clams in offers some evidence to support this prediction. residence adjacent to the polder. SAV and particulate Liberty Island sits in the middle of a complex of organic matter promote epibenthic invertebrates. historical and created sloughs, including Cache Piscivorous and benthic feeders perform well in these Slough, Lindsey Slough, Shag Slough, the Toe Drain, tracts (Nobriga et al. 2005; Nobriga and Feyrer 2007; and the Sacramento Deep Water Ship Channel. M. Young and D. DeCarion, 2010–2017 unpublished The north end of Liberty Island has an emergent data, see "Notes"). Warm temperatures, abundant freshwater marsh, dominated by tules, that is directly structure, and clear water favor alien centrarchids, connected to the open water of the tract. Liberty including . Island undoubtedly receives ecological benefits from the heterogeneity of the region, including cold The east Delta will be characterized by moderate water refugia, inputs from the marsh, and pelagic flows, moderate elevation, and low turbidity. NSBI production from adjacent regions. Pulses of high- scores are somewhat higher than the outh Delta’s. nutrient water from the Sacramento River and the Although the east Delta will resemble the south produce ephemeral phytoplankton Delta in many respects, the east Delta will be blooms. It has less extensive SAV and clam ebb‑dominated rather than flood-dominated (because abundance than other flooded tracts to the south. of differences in water operations), and sit adjacent Nitrogen inputs are limited in this area relative to to an elevation gradient into transitional intertidal other regions in the Delta and appear subject to rapid and floodplain habitats. I characterized this as a draw-down. Liberty Island appears to have a high transition zone because of the potential to capitalize proportion of native to alien fishes, particularly in on flow energy, seasonal floodplain activation as wet years. Abundant planktivores are found in the a food resource, and elevation to create unique region, including Delta Smelt, Threadfin Shad and outcomes. Left alone, polders here will be expected to American Shad, consistent with NSBI predictions follow a pathway similar to those in the south Delta. (Lindberg and Marzuola 1993; Sommer et al. 2011; However, careful management of breaches, structure, Sommer and Mejia 2013). flow, and residence time will create very different habitats. In addition, this region may lend itself to The south Delta contains many of the lowest-scoring subsidence reversal management, such as that in polders. These are characterized by low flows, deep progress on Twitchell Island. Such activities would subsidence, and low turbidity, attributes resembling help to create a barrier between polder ecosystems a freshwater lake. Flows will be flood-dominated dominated by alien species in the south and the

16 DECEMBER 2017 mixed-community polder ecosystems in the north Physical Structure and west Delta. There are currently no flooded tracts in this region, but the model suggests that most Structure may consist of dike edges, SAV, wood, flooded polders would support a mix of native and or any other surface. Epibenthic invertebrates use alien benthic and piscivorous fishes. The effectiveness structure for a substrate. Predator and prey fishes of the polders would be determined, in part, by alike use structure for refuge and predation, including design and management decisions. structure provided by SAV. Thick stands of E. densa can favor alien fishes over natives (Brown 2003; Feyrer 2004; Nobriga et al. 2005; Nobriga and Feyrer Limitations of the Study and Further Research 2007). Complex, varied structure, such as fallen The NSBI was designed to evaluate the response trees, or native SAV such as Stuckenia spp., offers of individual polders to flooding — something that opportunities for balanced interactions among trophic may be inevitable for many of them — and the guilds to occur. environmental consequences of such an event. I based the three metrics used here upon available Nutrient Inputs and Phytoplankton Production data that were suitable to generalization over a large area. However, these generalizations are Much of the estuary is subject to high nutrient bound to be conditional for each polder site; to loads. Nutrient enrichment can create phytoplankton understand outcomes more precisely would involve growth, yet blooms seldom occur in the estuary detailed modeling. Additional metrics that will bear today, in part as a result of clam grazing. The clams consideration for each polder will be connectivity are abundant and usually food-limited (Foe and and geomorphology, physical structure, nutrient Knight 1985), suggesting that they have the capacity inputs, temperature range, and salinity. I discuss to consume much of the available phytoplankton. these below. Portions of the Delta tend to have less E. densa and fewer clams (Suisun Marsh, Liberty Island, the CLC). Phytoplankton blooms have been observed to occur Exchange and Geomorphology under moderate nutrient conditions, but dissipate The exchange of nutrients and production is a as they (1) run out of nutrients, (2) settle out of the function of the number of breaches, as well as the water column to the sediment layer, or (3) become shape and depth of the polder. Long profiles relative grazed by clams as they moved toward the western to the tidal exchange create mixed residence times Delta. and mechanisms for particle retention within the sloughs (Enright et al. 2006, unreferenced, see Temperature Range “Notes”; Enright 2008, 2010, unreferenced, see “Notes”; Enright et al. 2013). Rates of exchange that Thermal refuges have become more critical because are variable are likely to best support restoration climate change may increase summer surface water habitat. Complete (high) exchange is unlikely to temperatures close to or beyond the physiological support sufficient residence time to build up blooms capacity of many native fish (Dettinger 2005; of plankton. Low exchange may support blooms, Dettinger and Culberson 2008; Nobriga et al. 2008). but will cause drawdown of nutrients without Deep pools offer cool temperature refuges that allow replenishment, and limit distribution of food to other vulnerable fishes to survive. regions (i.e., open habitat) where it can be used by grazers and predators (Lucas et al. 1999a, 1999b, Salinity 2002; Ahearn et al. 2006; Doyle 2010; Lucas and Thompson 2012). Polders that support exchange None of the Delta’s fish species depend exclusively which varies on a lunar tidal scale are likely to on brackish water, but salinity structures habitat in support pelagic production and fishes. a way that promotes diversity. Most native species are remarkably tolerant to changes in salinity, while many invasives are less tolerant (Feyrer 2004; Feyrer

17 https://doi.org/10.15447/sfews.2017v15iss4art4 SAN FRANCISCO ESTUARY & WATERSHED SCIENCE VOLUME 15, ISSUE 4, ARTICLE 4 et al. 2005, 2006, 2007; Nobriga et al. 2008). Tidal site to reduce ecological effects — before catastrophic restoration projects in the low-salinity zone (i.e., flooding. values around 2 psu) are subject to varying salinity, which may preferentially support native species to Designing Polders some degree. Through management and proper habitat design, All of these factors will need to be modeled on a the function of flooded polders may be improved, polder-by-polder basis to enable a clear prediction of particularly if ecological goals are scaled suitably how each will develop into aquatic habitat. Although to the available ecosystem. Design goals (that is, such an approach is unpractical on a Delta-wide measurable outcomes) for flooded polders may basis, it should be used to evaluate polders targeted include increased pelagic productivity, reduced for restoration by breaching, or polders that are at extent of alien SAV, reduced alien clam abundance high risk of flooding with low probability of repair. and distribution, and a suite of native or desirable These latter cases are discussed in the next section. alien fishes. Not all of these desirable outcomes are attainable from any given flooded polder. Some Cross Comparison of Economic and Logistic of these habitat outcomes may support restoration Rankings with Habitat Scoring goals for the Delta, while others will be neutral or antagonistic to those goals. Restoration goals should Some polders have been prioritized for repair and be chosen that scale to the physical constraints of preservation in case of flooding because they the site, and which work in synergy with adjacent are important for urban populations, salinity aquatic habitat. management, or water export. Others may be repaired because of the economic value of the land. To maximize expensive investments for longevity and function, most flooded polders will require careful Of the polders with high NSBI scores, a number are planning, design, and management. Planning will already flooded, including Sherman Lake, Liberty need to incorporate regional concerns. The increase Island, and . Van Sickle Island is in volume of aquatic habitat has implications for a managed wetland. The non-flooded tracts are used tidal excursion and directional flows. Undesirable primarily for agriculture, although Prospect Island is species may encroach, complicating recovery efforts planned to be flooded for use as native fish habitat. for endangered species, and water quality may Both the probability of failure and the prioritization be affected, particularly if hydrodynamic shifts of repairs for non-flooded islands in this group are increase salt incursion and nutrient availability. low. This suggests that the rare breach and flood on Finally, planning must also anticipate risks to these islands will tend to become permanent. The adjacent non-flooded polders whose levees may be exception to this may be Van Sickle Island, which, subject to from increased wave action and because it is managed for ponds and waterfowl, underground seepage. Environmental reviews and and is quite shallow, may be repaired nearly as permits will be required to satisfy legal requirements easily as it is breached. For the other islands, repair, under the Endangered Species Act, the Clean Water de-watering, and rehabilitation once flooded may not Act, the California Environmental Quality Act, the be economically feasible. National Environmental Protection Act, and the Delta Many of the polders with the lowest NSBI scores Protection Act (Suddeth 2011). have low repair prioritizations, and generally high Design and management of flooded polders will vary probabilities for failure, suggesting that a number depending upon desired outcomes. As presented here, of these tracts may also fail and not be repaired. As regional constraints will be critical to the success suggested above, it would be helpful to use a full of outcomes. For example, in a tidally driven area suite of modeling tools to carefully evaluate these like the CLC, polders that are designed to support high-risk polders for environmental outcomes. This pelagic food webs will require scaling to the tidal would allow managers and stakeholders to begin energy available in that region. However, in a high- planning — including approaches to manipulate the flow region like the Confluence, breaches may need

18 DECEMBER 2017 to be replaced with configurable gates to control experimental comparisons between treatments; for flow rate. In the south Delta, it may be desirable to example, pond versus slough performance. breach tracts and allow an ecosystem dominated by Figure 11 shows a more highly managed option aliens to colonize it, creating lake-like environments that might be suitable for the transition zone in the dominated by invasive aquatic plants and alien east Delta. The design also incorporates replicate fishes like largemouth bass. Passive designs, while treatments, in this case two built sloughs with inexpensive and not incompatible with recreational terminal, gated ends, which can be spilled into a uses, still incorporate considerable risks if unintended deeply subsided floodplain. The sloughs can be consequences occur. For example, infestations of manipulated to test the effect on production of E. densa that impede navigation, or blooms of residence time, tidal exchange, or nutrient additions. harmful algae such as Microcystis aeruginosa that The floodplain would be intensively managed with threaten public health, may be difficult to manage tules, rice, or some other wetland vegetation to without appropriate management and supporting support soil accretion. design features. Design tools can include the number and location CONCLUSIONS of breaches, the installation of maneuverable gates to manage water exchange, the creation of starter Regional differences are important for managing channels to promote water flow paths, the addition current and future flooded polder habitats in the of sediment berms to support emergent vegetation Delta. Flooded polders in the north Delta and CLC and control water flow , installation of facilities to will be best managed as river or tidal support recreation and science, the eradication of sloughs. The Confluence, with intensive management, undesirable vegetation, and the planting of desirable may be operated as productive open-water estuarine vegetation. Because of unknowns, features to support habitat. The south Delta has little potential for adaptive management experiments would be highly conservation, so it may be best to manage it as desirable, including subdividing tracts into separate a novel lake ecosystem, with an emphasis on ponds that could be used for comparative treatments. preserving water transport and recreation. The transition zone in the east Delta serves as both Figure 10 demonstrates a flooded polder designed connector and buffer between these two dramatically to support adaptive management by creating different ecosystems. Decisions on flooded polder three parallel ponds that can be used to deploy management should be considered within this experimental treatments. Configurable gates regional context. at strategic locations allow water flow to be manipulated. For example, gates can be set to drive Decommissioning and flooding of polders throughout one-way flow pulses scaled to tidal cycles, which can the Delta will occur by accident or intention. slow the movement of water across a site, potentially Unfortunately, the polders most likely to flood and increasing the production and accumulation of become abandoned also offer the fewest conservation pelagic food. An alternative setting leaves gates open benefits, particularly in the south Delta. There are to bi-directional flows, leaving the site completely few economic incentives to prepare for aggressive open to tidal exchange, which may facilitate passage management of these tracts, unless the cost of future of fish, but also increases rapid dispersion and risks is considered. These risks include barriers to advection of food resources. A third option could navigation, development of harmful algal blooms, allow mimicry of historic slough variability and water quality degradation, and risks to threatened function by allowing water to move through side and endangered species. Investments in Delta polder gates and hold in different ponds. Gate manipulations management must be considered not only in the light offer the opportunity to maximize desired outcomes of land value, but also in terms of potential losses and to run experiments that measure ecosystem and gains. response in water quality, food production and It is worth noting that polders planned for restoration fish usage. Different configurations would allow benefits may be benign or productive after initial

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Figure 10 Dike and gate configuration so support one-way flows across replicate ponds, or tidal, two-way flows along historic slough pathways

Figure 11 Configurable sloughs with spillways to experimental floodplain on a deeply subsided island

20 DECEMBER 2017 flooding, but may lose their conservation potential Dettinger MD, Culberson S. 2008. Internalizing climate without proper interventions. Up-front investment change—scientific resource management and the climate and continuous ongoing management will be change challenges. San Franc Estuary Watershed Sci required for all subsided polders, whether flooded [Internet]. [cited 2017 Oct 01]; 6(2). Available from: or not. The tools of adaptive management offer https://escholarship.org/uc/item/64z013q3 the benefits of strategic planning, investment, and https://doi.org/10.15447/sfews.2008v6iss2art5 infrastructure design and are better options for Doyle L. 2010. A three-dimensional water quality model risk management, better habitat and recreation for estuary environments [dissertation] [Internet]. Davis opportunities, and increased scientific understanding. (CA): University of California, Davis; [cited 2017 Oct 01]. Available from: ACKNOWLEDGEMENTS http://search.proquest.com/docview/872551274 This work was supported by the UC Davis Center Durand J, Fleenor W, McElreath R, Santos MJ, for Watershed Sciences and the Stephen Bechtel, Moyle P. 2016. Physical controls on the distribution Jr. Foundation. Thanks to Bill Fleenor for use of of the submersed aquatic weed Egeria densa in modeling data, to the Moyle lab, for feedback and the Sacramento–San Joaquin Delta, California and discussion, and to Burak Yikilmaz, who helped with Implications for Habitat Restoration. San Franc Estuary visualizations. The manuscript was greatly improved Watershed Sci [Internet]. [cited 2017 Oct 01]; 14(1). by comments from Peter Moyle, Jeff Mount, and Available from: Randy Dahlgren. https://escholarship.org/uc/item/85c9h479 https://doi.org/10.15447/sfews.2016v14iss1art4 REFERENCES Durand JR. 2015. A conceptual model of the aquatic food web of the upper San Francisco Estuary. San Franc Ahearn DS, Viers JH, Mount JF, Dahlgren RA. 2006. Estuary Watershed Sci [Internet]. [cited 2017 Oct 01]; Priming the productivity pump: flood pulse driven trends 13(3). Available from: in suspended algal biomass distribution across a restored https://escholarship.org/uc/item/0gw2884c floodplain. Freshw Biol [Internet]. [cited 2017 Oct 01]; https://doi.org/10.15447/sfews.2015v13iss3art5 51(8):1417–1433. Available from: http://onlinelibrary. wiley.com/doi/10.1111/j.1365-2427.2006.01580.x/full Enright C, Culberson SD, Burau JR. 2013. Broad timescale https://doi.org/10.1111/j.1365-2427.2006.01580.x forcing and geomorphic mediation of tidal marsh flow and temperature dynamics. Estuaries Coasts [Internet]. Brown LR. 2003. Will tidal wetland restoration enhance [cited 2017 Oct 01];36(6):1319–1339. Available from: populations of native fishes? San Franc Estuary https://doi.org/10.1007/s12237-013-9639-7 Watershed Sci [Internet]. [cited 2017 Oct 01]; 1(1). Available from: Ferrari MCO, Ranåker L, Weinersmith KL, Young MJ, https://escholarship.org/uc/item/2cp4d8wk Sih A, Conrad JL. 2014. Effects of turbidity and https://dx.doi.org/10.15447/sfews.2003v1iss1art2 an invasive waterweed on predation by introduced largemouth bass. Environ Biol Fishes [Internet]. [cited Conomos TJ, Smith RE, Gartner JW. 1985. Environmental 2017 Oct 01]; 97(1):79–90. Available from: http://link. setting of . Hydrobiologia [Internet]. springer.com/article/10.1007%2Fs10641-013-0125-7 [cited 2017 Oct 01]; 129(1):1–12. Available from: https://doi.org/10.1007/s10641-013-0125-7 https://doi.org/10.1007/BF00048684 Feyrer F. 2004. Ecological segregation of native and alien Dettinger MD. 2005. From climate-change spaghetti to larval fish assemblages in the southern Sacramento–San climate-change distributions for 21st century California. Joaquin Delta. In: Feyrer F, Orsi J, Brown LR, Brown RL, San Franc Estuary Watershed Sci [Internet]. [cited 2017 editors. Early life history of fishes in the San Francisco Oct 01]; 3(1). Available from: Estuary and Watershed. Bethesda (MD): American https://escholarship.org/uc/item/2pg6c039 Fisheries Society Symposium. p. 67–79. https://doi.org/10.15447/sfews.2005v3iss1art6

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